GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cmtB in Escherichia coli BW25113

Align Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate 17660 b3599 fused mannitol-specific PTS enzymes: IIA components/IIB components/IIC components (NCBI)

Query= TCDB::C0H3V2
         (143 letters)



>FitnessBrowser__Keio:17660
          Length = 637

 Score =  118 bits (296), Expect = 1e-31
 Identities = 56/137 (40%), Positives = 89/137 (64%), Gaps = 2/137 (1%)

Query: 4   LAKENIKLNQTVSSKEEAIKLAGQTLIDNGYVTEDYISKMFEREETSSTFMGNFIAIPHG 63
           L  ENI L +  ++KEEAI+ AG+ L+  GYV  +Y+  M +RE+ + T++G  IA+PHG
Sbjct: 496 LGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLGESIAVPHG 555

Query: 64  TEEAKSEVLHSGISIIQIPEGVEYG--EGNTAKVVFGIAGKNNEHLDILSNIAIICSEEE 121
           T EAK  VL +G+   Q PEGV +G  E + A++V GIA +NNEH+ +++++     +E 
Sbjct: 556 TVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSLTNALDDES 615

Query: 122 NIERLISAKSEEDLIAI 138
            IERL    S ++++ +
Sbjct: 616 VIERLAHTTSVDEVLEL 632


Lambda     K      H
   0.310    0.130    0.342 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 179
Number of extensions: 6
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 143
Length of database: 637
Length adjustment: 26
Effective length of query: 117
Effective length of database: 611
Effective search space:    71487
Effective search space used:    71487
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory